Rename namespaces and other identifiers in the codebase

[rfairley]

Describe the feature

From (#121):

Decide on a few key namespaces to group things by
Reason: As we grow our code base, we will have new peripherals, data structures, algorithms, etc. We should agree on namespaces these things should go in, otherwise things will get hard to maintain fast

Also, rename files, namespaces, classes, and functions, and any other identifers that are prominent in documentation throughout the codebase. This must be done after the naming convention in (#158) has been finalized.

Reason for request
Tidier codebase, cleaner documentation. Both developers and readers of the documentation need this.

Timeline
Discuss and decide what the namespaces are with the team by end of January.
First week of February before next "release" - merge

Additional information
Blocked by the naming style part of (#158).